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http://ontologist.com 1/24
An ontology-based methodology for the migration of biomedical terminologies to the EHR
Barry Smith and Werner Ceusters
http://ontologist.com 3/24
The concept diabetes mellitus becomes ‘associated with a diabetic patient’
concept patient concept diabetes
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?
The concept diabetes mellitus becomes ‘associated with a diabetic patient’
?
concept patient concept diabetes
what it is on the
side of the patient
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Jane’s favourite supermarket
July 4th, 1990: Jane goes shopping:
The freezer section of Jane’s favourite supermarket
The only available warning sign used outside
A very suspiciously shaped upper leg
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A visit to the hospital City Health Centre Dr. Peters
(City HC) Dr. Longley
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Standard EHRs
Specific codes for: patients, physicians, times, places, sometimes to X-ray images
General codes for everything else
The record tells us that there is some instance of the class the code refers to
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5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
Different patients, same fracture codes:Same (numerically identical) fracture ?
Same patient, different dates, same fracture
codes: same (numerically identical)
fracture ?
Same patient, same date,2 different fracture codes:
same (numerically identical) fracture ?
ProblemsDifferent patients. Same supermarket? Same freezer section?
Same patient, different dates, Different codes. Same (numericallyidentical) polyp ?
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Difficult to:
count the number of (numerically) different diseases (bad statistics on incidence, prevalence, cost ...)
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Difficult to:relate (numerically the same or different) causal factors to disorders:
Dangerous public places (swimming pools)
HIV contaminated blood
food from unhygienic source, ...
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The solution
unique numerical IDs for all concrete individual entities relevant to the
diagnosis and therapy of each patient
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Referent tracking already used as a matter of course for
bank and credit card transactions
Fedex / UPS parcels
cargo
conveyor belt manufacturing
mp3 files (for Digital Rights Management)
archeological specimens
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types / concepts instances / particulars
scientific texts, dictionariesdiaries, biographies, histories, journalism
medical ontologies, terminologies
clinical records
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types
rabbit, headache, human being, salute, death
Mary’s rabbit, my current headache, me, Rumsfeld’s salute at 4pm on 6/22/04, Reagan’s death
instances
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Referent Tracking
Method: introduce an Instance Unique Identifier (IUI) for each relevant individual entity
Outcome: An ever growing map of clinical cases, and of their interrelations to other clinical cases
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Services
– IUI generator– IUI assignment (facility now in openEHR)– IUI repository– Referent Tracking Database (RTDB):
statements relating instances to instances and types
software now availablewill be tested in a clinical setting
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Conclusion 1/4Referent tracking can solve a number of
problems in an elegant wayExisting coding systems and technologies
can be used for the implementationThe use of Health Card technology will
make the assignment of IUIs very easy to implement
Use of randomly assigned alphanumeric IDs can also bring data security advantages
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Conclusion 2/4
because the same patient often attends different hospitals using different coding systems the use of common IUI repositories will gradually lead to automatic mappings between terminologies
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Conclusion 3/4
as IUIs come to be associated with a plurality of codes from different coding systems we can run statistical tests to find outliers – codes which were misapplied; or ill-definedor to test and enhance rules for reasoning postulated by coding systems such as SNOMED-CT